The Indians didn't necessarily pick their best eligible prospects (aside from Aubrey and Snyder, of course); they picked the prospects most likely to be picked in the Rule 5 draft. The two relievers (Perez and Mujica) could have been stashed quite easily in someone's bullpen; Perez especially would be enticing.
The interesting pick from my standpoint was Brian Slocum. He had a decent season in Akron, but perhaps his strong showing in Arizona was what put him on the roster. He held AFL hitters to a .192 average, quite a feat considering the talent level of his opponents.
I'll explore the eligibles not protected at a later date, but feel free to talk about it here. I'm going out of town for the weekend, so I'll see you guys on Monday.
UPDATE: Lost in the debris of this story, the Indians did not put Billy Traber back on the 40-man roster. As a result, Traber became a six-year minor league free agent and has signed with the Washington Nationals, who were willing to add him to their 40-man roster. I had a soft spot for Traber, who memorably one-hit the Yankees as a 23-year-old rookie in 2003, but with an injury situation I think you have to give the team's scouts and medical staff the benefit of the doubt. [Jay]